MolNFT v1 · #158898 · protein
Saccharomyces cerevisiae V-ATPase STV1-V1VO state 2
6O7W · V-type proton ATPase subunit D: “Saccharomyces cerevisiae V-ATPase STV1-V1VO state 2”. Electron microscopy, 20 pockets (best druggability 0.86). MolNFT v1 #158898 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6O7W
- Type
- protein
- Length
- 8,038 residues
- Chains
- 31
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- V-type proton ATPase subunit D; V-type proton ATPase subunit F; Vacuolar ATP synthase…
- UniProt
- P32610, P39111, B3LH69, P16140, P48836, P22203, P41807, P31412, P37296, P53262, P23968, P32366, P25515, P32842, Q3E7B6, P0C5R9
- Pockets
- 20 · best druggability 0.86
Structure
electron microscopy · 20 distinct chains · 61% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| M | V-type proton ATPase subunit D | protein | 210 | 75% helix, 9% strand | P32610 |
| N | V-type proton ATPase subunit F | protein | 115 | 37% helix, 22% strand | P39111 |
| C, E, A | Vacuolar ATP synthase catalytic subunit a | protein | 593 | 36% helix, 25% strand | B3LH69 |
| D, F, B | V-type proton ATPase subunit B | protein | 457 | 35% helix, 24% strand | P16140 |
| L, H, J | V-type proton ATPase subunit G | protein | 105 | 85% helix, 0% strand | P48836 |
| K, G, I | V-type proton ATPase subunit E | protein | 217 | 71% helix, 11% strand | P22203 |
| P | V-type proton ATPase subunit H | protein | 461 | 72% helix, 0% strand | P41807 |
| O | V-type proton ATPase subunit C | protein | 392 | 47% helix, 13% strand | P31412 |
| a | V-type proton ATPase subunit a, golgi isoform | protein | 625 | 65% helix, 5% strand | P37296 |
| b | V0 assembly protein 1 | protein | 44 | 59% helix, 0% strand | P53262 |
| c | V-type proton ATPase subunit C'' | protein | 197 | 81% helix, 0% strand | P23968 |
| d | V-type proton ATPase subunit D | protein | 343 | 56% helix, 0% strand | P32366 |
| g | V-type proton ATPase subunit C | protein | 153 | 80% helix, 0% strand | P25515 |
| h, i, l | V-type proton ATPase subunit C | protein | 157 | 77% helix, 0% strand | P25515 |
| j | V-type proton ATPase subunit C | protein | 156 | 75% helix, 0% strand | P25515 |
| k | V-type proton ATPase subunit C | protein | 158 | 76% helix, 0% strand | P25515 |
| m, n | V-type proton ATPase subunit C | protein | 158 | 74% helix, 0% strand | P25515 |
| o | V-type proton ATPase subunit C' | protein | 156 | 78% helix, 0% strand | P32842 |
| e | V-type proton ATPase subunit E | protein | 64 | 66% helix, 3% strand | Q3E7B6 |
| f | Putative protein YPR170W-B | protein | 61 | 70% helix, 0% strand | P0C5R9 |
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 975 | 0.86 | 0.87 | 141 | empty |
| 2 | 1091 | 0.85 | 0.87 | 181 | empty |
| 3 | 944 | 0.84 | 0.86 | 118 | empty |
| 4 | 1068 | 0.83 | 0.84 | 159 | empty |
| 5 | 1007 | 0.83 | 0.84 | 156 | empty |
Interfaces
55 interfaces between chains.
- A–B · 1619 Ų buried · 10 hydrogen bonds · protein-protein
- E–F · 1406 Ų buried · 8 hydrogen bonds · protein-protein
- D–E · 1075 Ų buried · 8 hydrogen bonds · protein-protein
- C–D · 1012 Ų buried · 6 hydrogen bonds · protein-protein
- J–I · 967 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6O7W · Saccharomyces cerevisiae V-ATPase Stv1-V1VO State 2 · the same entry in another collection · chain K against K, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P32610
- Every structure of UniProt P39111
- Every structure of UniProt B3LH69
- Every structure of UniProt P16140
- Every structure of UniProt P48836
- Every structure of UniProt P22203
- Every structure of UniProt P41807
- Every structure of UniProt P31412
- Every structure of UniProt P37296
- Every structure of UniProt P53262
- Every structure of UniProt P23968
- Every structure of UniProt P32366
- Every structure of UniProt P25515
- Every structure of UniProt P32842
- Every structure of UniProt Q3E7B6
- Every structure of UniProt P0C5R9
- Elsewhere: RCSB PDB 6O7W · PDBe 6O7W · UniProt P32610 · UniProt P39111 · UniProt B3LH69 · UniProt P16140 · UniProt P48836 · UniProt P22203 · UniProt P41807 · UniProt P31412 · UniProt P37296 · UniProt P53262 · UniProt P23968 · UniProt P32366 · UniProt P25515 · UniProt P32842 · UniProt Q3E7B6 · UniProt P0C5R9
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